LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
# pour particles into cone-shaped funnel, settle them, let them run out bottom

variable	name string funnel_pour

thermo_modify	flush yes
units 		si
variable	PI equal 3.141592653589
variable	seed equal 14314

###############################################
# Geometry-related parameters
###############################################

variable	xlo equal 10
variable	xhi equal 40
variable	ylo equal 10
variable	yhi equal 40
variable	zlo equal -20
variable	zhi equal 50

variable	xc equal 25
variable	yc equal 25

variable	zconehi equal 50
variable	zconelo equal 10
variable	zcyllo equal 0
variable	radconelo equal 2
variable	radconehi equal 20

################################################
# Particle sizes
################################################

variable	rlo equal 0.25
variable	rhi equal 0.5
variable	dlo equal 2.0*${rlo}
variable	dlo equal 2.0*0.25
variable	dhi equal 2.0*${rhi}
variable	dhi equal 2.0*0.5

variable 	skin equal ${rhi}
variable 	skin equal 0.5

###############################################
# Granular contact parameters
###############################################

variable	coeffRes equal 0.1
variable	coeffFric equal 0.5

variable	density equal 1.0
variable	EYoung equal 10^5
variable 	Poisson equal 2.0/7.0
variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
variable	GShear equal 100000/(2*(1+${Poisson}))
variable	GShear equal 100000/(2*(1+0.285714285714286))

variable	gravity equal 1.0

variable	reff equal 0.5*(${rhi}+${rlo})
variable	reff equal 0.5*(0.5+${rlo})
variable	reff equal 0.5*(0.5+0.25)
variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5

## Typical way to set kn, kt, etc.:
variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable        kt equal 4.0*${GShear}/(2-${Poisson})
variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)

variable	a equal (-2.0*log(${coeffRes})/${PI})^2
variable	a equal (-2.0*log(0.1)/${PI})^2
variable	a equal (-2.0*log(0.1)/3.141592653589)^2
variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable        gamma_t equal ${gamma_n}*0.5
variable        gamma_t equal 903.503751814138*0.5

variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)

variable	dt equal ${tcol}*0.05
variable	dt equal 0.00210943016014969*0.05
timestep	${dt}
timestep	0.000105471508007485

###############################################
variable	dumpfreq equal 1000
variable	logfreq equal 1000

newton 		off
atom_style	sphere

boundary	p p f

region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region		boxreg block 10 40 10 40 ${zlo} ${zhi}
region		boxreg block 10 40 10 40 -20 ${zhi}
region		boxreg block 10 40 10 40 -20 50
create_box	1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
  1 by 1 by 1 MPI processor grid

pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff	* *

neighbor        ${skin} multi
neighbor        0.5 multi
thermo 		${logfreq}
thermo 		1000

comm_style	brick
comm_modify 	mode multi group all vel yes
balance		1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 0
  ghost atom cutoff = 0
  binsize = 30, bins = 1 1 3
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair gran/hertz/history, perpetual
      attributes: half, newton off, size, history
      pair build: half/size/multi/atomonly/newtoff
      stencil: full/multi/3d
      bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
fix		bal all balance 10000 1.1 shift xyz 20 1.01

####################### Options specific to pouring #########################

# insertion region for fix/pour

region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
region	     	insreg cylinder z 25 25 10 30 50 side in units box

# define cone and cylinder regions - see lammps doc on region command
# note new open options

region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 

region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 

region		hopreg union 2 conereg cylreg

fix		grav all gravity ${gravity} vector 0 0 -1
fix		grav all gravity 1 vector 0 0 -1
fix		1 all nve/sphere


fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg

fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1

#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z

#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
#dump_modify	2 pad 6

thermo_style	custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
thermo_modify	flush yes lost warn

# Initial run to fill up the cone

run		20000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 3000 every 59965 steps, 2000 by step 1
Per MPI rank memory allocation (min/avg/max) = 6.648 | 6.648 | 6.648 Mbytes
   Step          CPU          Atoms        KinEng    
         0   0                      0  -0            
      1000   0.42422547          2000  -0            
      2000   0.61303447          2000  -0            
      3000   0.80093891          2000  -0            
      4000   0.9870726           2000  -0            
      5000   1.174735            2000  -0            
      6000   1.3615338           2000  -0            
      7000   1.5481574           2000  -0            
      8000   1.7332676           2000  -0            
      9000   1.9202086           2000  -0            
     10000   2.1067651           2000  -0            
     11000   2.2904529           2000  -0            
     12000   2.4750549           2000  -0            
     13000   2.6588335           2000  -0            
     14000   2.8432942           2000  -0            
     15000   3.0276634           2000  -0            
     16000   3.2143893           2000  -0            
     17000   3.3989855           2000  -0            
     18000   3.5835207           2000  -0            
     19000   3.7684773           2000  -0            
     20000   3.9550272           2000  -0            
Loop time of 3.95505 on 1 procs for 20000 steps with 2000 atoms

99.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.40709    | 0.40709    | 0.40709    |   0.0 | 10.29
Neigh   | 0.065613   | 0.065613   | 0.065613   |   0.0 |  1.66
Comm    | 0.0076015  | 0.0076015  | 0.0076015  |   0.0 |  0.19
Output  | 0.00041671 | 0.00041671 | 0.00041671 |   0.0 |  0.01
Modify  | 3.3895     | 3.3895     | 3.3895     |   0.0 | 85.70
Other   |            | 0.08486    |            |       |  2.15

Nlocal:           2000 ave        2000 max        2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           1607 ave        1607 max        1607 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1607
Ave neighs/atom = 0.8035
Neighbor list builds = 71
Dangerous builds = 0
unfix 		ins
run		150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
   Step          CPU          Atoms        KinEng    
     20000   0                   2000   6652.2957    
     21000   0.18540841          2000   6807.2201    
     22000   0.37080157          2000   6973.9359    
     23000   0.55573123          2000   7142.3648    
     24000   0.74112501          2000   7276.9717    
     25000   0.92686283          2000   7369.4191    
     26000   1.1145958           2000   7497.6526    
     27000   1.3033904           2000   7638.946     
     28000   1.4921406           2000   7780.0339    
     29000   1.6824098           2000   7881.8177    
     30000   1.8751801           2000   7967.2641    
     31000   2.0698118           2000   7994.9273    
     32000   2.2682778           2000   7937.0671    
     33000   2.4695819           2000   7774.0508    
     34000   2.675988            2000   7591.1491    
     35000   2.886376            2000   7357.5176    
     36000   3.102007            2000   7147.2024    
     37000   3.321435            2000   6979.1604    
     38000   3.5426417           2000   6813.2152    
     39000   3.7660203           2000   6660.2701    
     40000   3.998044            2000   6502.8957    
     41000   4.234151            2000   6324.3951    
     42000   4.4731702           2000   6132.7516    
     43000   4.7137403           2000   5913.1841    
     44000   4.9572451           2000   5732.2095    
     45000   5.2042391           2000   5508.8322    
     46000   5.462849            2000   5306.8932    
     47000   5.724072            2000   5152.0521    
     48000   5.987507            2000   5028.2274    
     49000   6.2495317           2000   4896.102     
     50000   6.5151951           2000   4723.5189    
     51000   6.7809368           2000   4583.7526    
     52000   7.0554059           2000   4447.0187    
     53000   7.5371151           2000   4303.2307    
     54000   7.8249388           2000   4168.5251    
     55000   8.1204418           2000   4036.9704    
     56000   8.4176628           2000   3901.1183    
     57000   8.7222873           2000   3716.7071    
     58000   9.0346411           2000   3473.5422    
     59000   9.3526758           2000   3245.1223    
     60000   9.6699173           2000   3039.7845    
     61000   9.9903491           2000   2780.0187    
     62000   10.318591           2000   2577.3345    
     63000   10.65279            2000   2346.2488    
     64000   10.993148           2000   2116.7298    
     65000   11.335466           2000   1903.7828    
     66000   11.686936           2000   1631.1676    
     67000   12.046515           2000   1431.0198    
     68000   12.413611           2000   1212.875     
     69000   12.783883           2000   995.45046    
     70000   13.156707           2000   811.54766    
     71000   13.532628           2000   624.08622    
     72000   13.91241            2000   471.00862    
     73000   14.296186           2000   358.33486    
     74000   14.680961           2000   284.39416    
     75000   15.06644            2000   234.26671    
     76000   15.447805           2000   185.61836    
     77000   15.825601           2000   152.95918    
     78000   16.205661           2000   122.49023    
     79000   16.582292           2000   102.29396    
     80000   16.96433            2000   86.284684    
     81000   17.347289           2000   73.984781    
     82000   17.739993           2000   63.042918    
     83000   18.142078           2000   53.338428    
     84000   18.547853           2000   45.89585     
     85000   18.95343            2000   40.412826    
     86000   19.35904            2000   34.183381    
     87000   19.765916           2000   29.671524    
     88000   20.18651            2000   26.90414     
     89000   20.598969           2000   24.362631    
     90000   21.016445           2000   21.887341    
     91000   21.437072           2000   19.985662    
     92000   21.86331            2000   18.728162    
     93000   22.291217           2000   16.99941     
     94000   22.724102           2000   15.71941     
     95000   23.155367           2000   14.744057    
     96000   23.590722           2000   14.214918    
     97000   24.028273           2000   13.450182    
     98000   24.47017            2000   12.79222     
     99000   24.913929           2000   12.10595     
    100000   25.361256           2000   11.281863    
    101000   25.807117           2000   10.025419    
    102000   26.257292           2000   9.9574468    
    103000   26.70767            2000   9.4078117    
    104000   27.161728           2000   8.9079161    
    105000   27.617856           2000   8.6269302    
    106000   28.069631           2000   8.5512649    
    107000   28.526606           2000   8.4703948    
    108000   28.982832           2000   8.2747542    
    109000   29.441422           2000   8.2895118    
    110000   29.906198           2000   8.1785613    
    111000   30.36715            2000   7.8443234    
    112000   30.829642           2000   7.7436124    
    113000   31.319634           2000   7.8118604    
    114000   31.791602           2000   7.3806177    
    115000   32.260138           2000   7.0857235    
    116000   32.725698           2000   7.1346752    
    117000   33.192963           2000   7.0653751    
    118000   33.661517           2000   6.6314104    
    119000   34.127108           2000   6.2169614    
    120000   34.597123           2000   5.8988829    
    121000   35.064919           2000   5.4197277    
    122000   35.535855           2000   4.6381303    
    123000   36.005284           2000   4.4949206    
    124000   36.47519            2000   4.4261118    
    125000   36.945117           2000   4.4223703    
    126000   37.417732           2000   4.4858898    
    127000   37.888171           2000   4.3312536    
    128000   38.360713           2000   3.7124973    
    129000   38.835798           2000   3.5467396    
    130000   39.311234           2000   3.5104139    
    131000   39.783409           2000   3.5725612    
    132000   40.255871           2000   3.669455     
    133000   40.728998           2000   3.6168912    
    134000   41.203148           2000   3.3598517    
    135000   41.677786           2000   3.3743407    
    136000   42.15241            2000   3.1109764    
    137000   42.627707           2000   3.0720146    
    138000   43.100904           2000   3.1303776    
    139000   43.574775           2000   3.2052806    
    140000   44.050804           2000   2.8958882    
    141000   44.525409           2000   2.9931572    
    142000   44.999822           2000   3.0967832    
    143000   45.476054           2000   3.0576365    
    144000   45.951361           2000   3.2016943    
    145000   46.429655           2000   3.3817709    
    146000   46.905577           2000   3.4527239    
    147000   47.38743            2000   3.5928733    
    148000   47.86409            2000   3.7784682    
    149000   48.342003           2000   3.6587944    
    150000   48.823792           2000   3.7945669    
    151000   49.30105            2000   3.5551557    
    152000   49.780315           2000   3.6248848    
    153000   50.257553           2000   3.7361463    
    154000   50.737624           2000   3.8534319    
    155000   51.218208           2000   4.0101408    
    156000   51.695675           2000   3.7670652    
    157000   52.176961           2000   3.1487676    
    158000   52.657466           2000   2.980076     
    159000   53.134109           2000   3.0350592    
    160000   53.615609           2000   3.125389     
    161000   54.093868           2000   2.7516115    
    162000   54.576681           2000   2.413911     
    163000   55.055496           2000   2.297713     
    164000   55.538174           2000   2.3190806    
    165000   56.020458           2000   2.2868879    
    166000   56.501206           2000   2.1658547    
    167000   56.983465           2000   1.7511071    
    168000   57.466833           2000   1.4112478    
    169000   57.949757           2000   1.3623558    
    170000   58.43349            2000   1.3701579    
Loop time of 58.4335 on 1 procs for 150000 steps with 2000 atoms

99.4% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 29.221     | 29.221     | 29.221     |   0.0 | 50.01
Neigh   | 0.57927    | 0.57927    | 0.57927    |   0.0 |  0.99
Comm    | 0.060749   | 0.060749   | 0.060749   |   0.0 |  0.10
Output  | 0.20563    | 0.20563    | 0.20563    |   0.0 |  0.35
Modify  | 27.674     | 27.674     | 27.674     |   0.0 | 47.36
Other   |            | 0.6922     |            |       |  1.18

Nlocal:           2000 ave        2000 max        2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          15308 ave       15308 max       15308 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 15308
Ave neighs/atom = 7.654
Neighbor list builds = 367
Dangerous builds = 0

# remove "plug" - need to redefine cylinder region & union

region	  	cylreg delete
region		hopreg delete
region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 

region		hopreg union 2 cylreg conereg

unfix		hopper3
fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg

run		100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
   Step          CPU          Atoms        KinEng    
    170000   0                   2000   1.3701579    
    171000   0.48431316          2000   2.3724823    
    172000   0.96523693          2000   3.5881441    
    173000   1.4349569           2000   5.3771633    
    174000   1.902564            2000   7.5896471    
    175000   2.3637344           2000   10.77251     
    176000   2.817277            2000   14.806868    
    177000   3.2682365           2000   19.607624    
    178000   3.7215391           2000   25.426227    
    179000   4.1716711           2000   32.23584     
    180000   4.621872            2000   39.930468    
    181000   5.0676618           2000   47.686304    
    182000   5.5105545           2000   56.506806    
    183000   5.9489081           2000   66.514326    
    184000   6.3843739           2000   77.554644    
    185000   6.8189889           2000   89.224002    
    186000   7.2526358           2000   102.07846    
    187000   7.6807565           2000   116.08141    
    188000   8.1050895           2000   130.97964    
    189000   8.52413             2000   146.77806    
    190000   8.9479211           2000   162.79858    
    191000   9.3652194           2000   179.02052    
    192000   9.780893            2000   196.26683    
    193000   10.192876           2000   214.38928    
    194000   10.606655           2000   232.32068    
    195000   11.018129           2000   251.74644    
    196000   11.424821           2000   272.25231    
    197000   11.833891           2000   294.64075    
    198000   12.237613           2000   318.32895    
    199000   12.640094           2000   342.44005    
    200000   13.045535           2000   368.35469    
    201000   13.445497           2000   395.2465     
    202000   13.85102            2000   422.63599    
    203000   14.254213           2000   450.45248    
    204000   14.654729           2000   479.60812    
    205000   15.057527           2000   510.44155    
    206000   15.456223           2000   543.25751    
    207000   15.849932           2000   577.35928    
    208000   16.240706           2000   612.29718    
    209000   16.629756           2000   647.8951     
    210000   17.019318           2000   683.79409    
    211000   17.40949            2000   720.36556    
    212000   17.802521           2000   759.27331    
    213000   18.192311           2000   798.27302    
    214000   18.582347           2000   837.93849    
    215000   18.970586           2000   877.92945    
    216000   19.362316           2000   919.62532    
    217000   19.755364           2000   962.83509    
    218000   20.146845           2000   1008.5243    
    219000   20.530427           2000   1054.5769    
    220000   20.914645           2000   1103.1843    
    221000   21.296153           2000   1153.0349    
    222000   21.681747           2000   1204.5599    
    223000   22.06794            2000   1257.1367    
    224000   22.45394            2000   1308.6735    
WARNING: Lost atoms: original 2000 current 1999 (../thermo.cpp:499)
    225000   22.843026           1999   1360.1205    
    226000   23.221639           1998   1404.8405    
    227000   23.603256           1996   1448.4869    
    228000   23.985547           1992   1491.8112    
    229000   24.359685           1985   1518.7013    
    230000   24.733284           1971   1507.6699    
    231000   25.100372           1965   1533.5096    
    232000   25.470109           1948   1489.4128    
    233000   25.840892           1933   1477.4536    
    234000   26.207893           1915   1425.8398    
    235000   26.570401           1904   1410.1451    
    236000   26.931189           1892   1401.7595    
    237000   27.28796            1880   1368.893     
    238000   27.642985           1868   1341.8885    
    239000   27.998754           1850   1286.7968    
    240000   28.353974           1833   1219.5123    
    241000   28.709461           1820   1173.3608    
    242000   29.065121           1806   1106.0727    
    243000   29.418519           1788   1035.912     
    244000   29.770812           1779   1021.6147    
    245000   30.11704            1767   969.40032    
    246000   30.457702           1757   939.12022    
    247000   30.800392           1739   840.9396     
    248000   31.141047           1730   822.06575    
    249000   31.483192           1719   762.11057    
    250000   31.831879           1707   708.50308    
    251000   32.176299           1700   692.12647    
    252000   32.520059           1697   694.5812     
    253000   32.884872           1686   652.36951    
    254000   33.229261           1682   662.95256    
    255000   33.557987           1677   637.34619    
    256000   33.891681           1672   630.71277    
    257000   34.230081           1669   641.87365    
    258000   34.571663           1665   635.862      
    259000   34.913723           1664   658.5339     
    260000   35.253805           1662   669.95468    
    261000   35.587547           1660   676.93495    
    262000   35.920661           1657   681.72646    
    263000   36.25079            1655   687.4078     
    264000   36.5838             1651   681.61352    
    265000   36.914146           1647   673.20622    
    266000   37.245414           1644   677.30073    
    267000   37.571588           1641   671.05897    
    268000   37.896337           1639   689.55776    
    269000   38.22279            1637   711.98809    
    270000   38.550831           1633   705.29974    
Loop time of 38.5508 on 1 procs for 100000 steps with 1633 atoms

99.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 20.145     | 20.145     | 20.145     |   0.0 | 52.25
Neigh   | 0.42523    | 0.42523    | 0.42523    |   0.0 |  1.10
Comm    | 0.042119   | 0.042119   | 0.042119   |   0.0 |  0.11
Output  | 0.0022978  | 0.0022978  | 0.0022978  |   0.0 |  0.01
Modify  | 17.495     | 17.495     | 17.495     |   0.0 | 45.38
Other   |            | 0.4416     |            |       |  1.15

Nlocal:           1633 ave        1633 max        1633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          11358 ave       11358 max       11358 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 11358
Ave neighs/atom = 6.955297
Neighbor list builds = 244
Dangerous builds = 0
Total wall time: 0:01:40
